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# 2017-11-07: added complete=FALSE to vcov.() call
exists.method <- function(generic, object, default=TRUE, strict=FALSE){
# this function copied from the Rcmdr package; won't be exported
classes <- class(object)
if (default) classes <- c(classes, "default")
if (strict) classes <- classes[1]
any(paste(generic, ".", classes, sep="") %in%
as.character(methods(generic)))
}
Predict <- function(object, ...){
if (exists.method("Predict", object, strict=TRUE))
UseMethod("Predict")
else if (!exists.method("predict", object, strict=TRUE) && exists.method("Predict", object))
UseMethod("Predict")
else UseMethod("predict")
}
# Predict.default <- function(object, ...){ # doesn't work correctly
# UseMethod("predict")
# }
Predict.lm <-function (object, newdata, se.fit = FALSE, scale = NULL, df = Inf,
interval = c("none", "confidence", "prediction"), level = 0.95,
type = c("response", "terms"), terms = NULL, na.action = na.pass,
pred.var = res.var/weights, weights = 1, vcov., ...) {
# modified version of stats::predict.lm()
# the next two local functions copied from stats package
qr.lm <- function (x, ...) {
if (is.null(r <- x$qr))
stop("lm object does not have a proper 'qr' component.\n Rank zero or should not have used lm(.., qr=FALSE).")
r
}
weights.default <- function (object, ...) {
wts <- object$weights
if (is.null(wts))
wts
else napredict(object$na.action, wts)
}
tt <- terms(object)
if (!inherits(object, "lm"))
warning("calling predict.lm(<fake-lm-object>) ...")
if (missing(newdata) || is.null(newdata)) {
mm <- X <- model.matrix(object)
mmDone <- TRUE
offset <- object$offset
}
else {
Terms <- delete.response(tt)
m <- model.frame(Terms, newdata, na.action = na.action,
xlev = object$xlevels)
if (!is.null(cl <- attr(Terms, "dataClasses")))
.checkMFClasses(cl, m)
X <- model.matrix(Terms, m, contrasts.arg = object$contrasts)
offset <- rep(0, nrow(X))
if (!is.null(off.num <- attr(tt, "offset")))
for (i in off.num) offset <- offset + eval(attr(tt, "variables")[[i + 1]], newdata)
if (!is.null(object$call$offset))
offset <- offset + eval(object$call$offset, newdata)
mmDone <- FALSE
}
n <- length(object$residuals)
p <- object$rank
p1 <- seq_len(p)
piv <- if (p)
qr.lm(object)$pivot[p1]
if (p < ncol(X) && !(missing(newdata) || is.null(newdata)))
warning("prediction from a rank-deficient fit may be misleading")
beta <- object$coefficients
predictor <- drop(X[, piv, drop = FALSE] %*% beta[piv])
if (!is.null(offset))
predictor <- predictor + offset
interval <- match.arg(interval)
if (interval == "prediction") {
if (missing(newdata))
warning("predictions on current data refer to _future_ responses\n")
if (missing(newdata) && missing(weights)) {
w <- weights.default(object)
if (!is.null(w)) {
weights <- w
warning("assuming prediction variance inversely proportional to weights used for fitting\n")
}
}
if (!missing(newdata) && missing(weights) && !is.null(object$weights) &&
missing(pred.var))
warning("Assuming constant prediction variance even though model fit is weighted\n")
if (inherits(weights, "formula")) {
if (length(weights) != 2L)
stop("'weights' as formula should be one-sided")
d <- if (missing(newdata) || is.null(newdata))
model.frame(object)
else newdata
weights <- eval(weights[[2L]], d, environment(weights))
}
}
type <- match.arg(type)
if (se.fit || interval != "none") {
w <- object$weights
res.var <- if (is.null(scale)) {
r <- object$residuals
rss <- sum(if (is.null(w)) r^2 else r^2 * w)
df <- object$df.residual
rss/df
}
else scale^2
if (type != "terms") {
if (p > 0) {
if (missing(vcov.)){
XRinv <- if (missing(newdata) && is.null(w))
qr.Q(qr.lm(object))[, p1, drop = FALSE]
else X[, piv] %*% qr.solve(qr.R(qr.lm(object))[p1, p1])
ip <- drop(XRinv^2 %*% rep(res.var, p))
}
else{
V <- if (is.function(vcov.)) vcov.(object)
else if (is.matrix(vcov.)) vcov.
else stop("vcov. must be a function or a matrix")
if (p < ncol(X)){
# rank-deficient case
b <- coef(object)
nms <- names(b[!is.na(b)])
X <- X[, nms]
}
ip <- diag(X %*% V %*% t(X))
}
}
else ip <- rep(0, n)
}
}
if (type == "terms") {
if (!missing(vcov.)) warning("vcov. argument not used for type='terms'")
if (!mmDone) {
mm <- model.matrix(object)
mmDone <- TRUE
}
aa <- attr(mm, "assign")
ll <- attr(tt, "term.labels")
hasintercept <- attr(tt, "intercept") > 0L
if (hasintercept)
ll <- c("(Intercept)", ll)
aaa <- factor(aa, labels = ll)
asgn <- split(order(aa), aaa)
if (hasintercept) {
asgn$"(Intercept)" <- NULL
avx <- colMeans(mm)
termsconst <- sum(avx[piv] * beta[piv])
}
nterms <- length(asgn)
if (nterms > 0) {
predictor <- matrix(ncol = nterms, nrow = NROW(X))
dimnames(predictor) <- list(rownames(X), names(asgn))
if (se.fit || interval != "none") {
ip <- matrix(ncol = nterms, nrow = NROW(X))
dimnames(ip) <- list(rownames(X), names(asgn))
Rinv <- qr.solve(qr.R(qr.lm(object))[p1, p1])
}
if (hasintercept)
X <- sweep(X, 2L, avx, check.margin = FALSE)
unpiv <- rep.int(0L, NCOL(X))
unpiv[piv] <- p1
for (i in seq.int(1L, nterms, length.out = nterms)) {
iipiv <- asgn[[i]]
ii <- unpiv[iipiv]
iipiv[ii == 0L] <- 0L
predictor[, i] <- if (any(iipiv > 0L))
X[, iipiv, drop = FALSE] %*% beta[iipiv]
else 0
if (se.fit || interval != "none")
ip[, i] <- if (any(iipiv > 0L))
as.matrix(X[, iipiv, drop = FALSE] %*%
Rinv[ii, , drop = FALSE])^2 %*% rep.int(res.var, p)
else 0
}
if (!is.null(terms)) {
predictor <- predictor[, terms, drop = FALSE]
if (se.fit)
ip <- ip[, terms, drop = FALSE]
}
}
else {
predictor <- ip <- matrix(0, n, 0L)
}
attr(predictor, "constant") <- if (hasintercept)
termsconst
else 0
}
if (interval != "none") {
tfrac <- qt((1 - level)/2, df)
hwid <- tfrac * switch(interval, confidence = sqrt(ip),
prediction = sqrt(ip + pred.var))
if (type != "terms") {
predictor <- cbind(predictor, predictor + hwid %o%
c(1, -1))
colnames(predictor) <- c("fit", "lwr", "upr")
}
else {
if (!is.null(terms))
hwid <- hwid[, terms, drop = FALSE]
lwr <- predictor + hwid
upr <- predictor - hwid
}
}
if (se.fit || interval != "none") {
se <- sqrt(ip)
if (type == "terms" && !is.null(terms) && !se.fit)
se <- se[, terms, drop = FALSE]
}
if (missing(newdata) && !is.null(na.act <- object$na.action)) {
predictor <- napredict(na.act, predictor)
if (se.fit)
se <- napredict(na.act, se)
}
if (type == "terms" && interval != "none") {
if (missing(newdata) && !is.null(na.act)) {
lwr <- napredict(na.act, lwr)
upr <- napredict(na.act, upr)
}
list(fit = predictor, se.fit = se, lwr = lwr, upr = upr,
df = df, residual.scale = sqrt(res.var))
}
else if (se.fit)
list(fit = predictor, se.fit = se, df = df, residual.scale = sqrt(res.var))
else predictor
}
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